NAME - EEDB::Chrom
SYNOPSIS
An object to encapsulate a Chromosome within an Assembly.
DESCRIPTION
An object that corresponds to specific chromosomes within an assembly. Because Chrom is tied to a specific assembly, an instance of a Chrom identifies not only the chromosome, but also the assembly and species
As with all objects in EEDB, Chrom interits from MQdb::DBObject and MQdb::MappedQuery. Please refer to these documents for all superclass methods
CONTACT
Jessica Severin <severin@gsc.riken.jp>
LICENSE
* Software License Agreement (BSD License)
* EdgeExpressDB [eeDB] system
* copyright (c) 2007-2009 Jessica Severin RIKEN OSC
* All rights reserved.
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
* * Neither the name of Jessica Severin RIKEN OSC nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ''AS IS'' AND ANY
* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL COPYRIGHT HOLDERS BE LIABLE FOR ANY
* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
set_cache_behaviour
Description : class level method to turn on/off global caching of Chromsome objects
since these are very small and used heavily, it is on my default
and it is recommended to not turn it off.
Parameter[1] : scalar 0/1 to turn the caching off/on
Returntype : none
Exceptions : none
get_cache_size
Description : get count of Chroms currently in the memory cache
Returntype : scalar count
Exceptions : none
init
Description: initialize a new instance of this object.
generally not needed for users to call this method
Returntype : $self
Exceptions : none
chrom_name
Description : simple getter/setter method for the chromosome name
Parameter[1] : <optional> if specififed it will set the chromsome name
Returntype : string
Exceptions : none
chrom_type
Description : simple getter/setter method for the chromosome type
Parameter[1] : <optional> if specififed it will set the chromsome type
Returntype : string
Exceptions : none
description
Description : simple getter/setter method for the chromosome description
Parameter[1] : <optional> if specififed it will set the chromsome description
Returntype : string
Exceptions : none
assembly
Description : simple getter/setter method for the Assembly of this Chrom
Parameter[1] : <optional> of type EEDB::Assembly. if specififed it will set the assembly
Returntype : EEDB::Assembly instance
Exceptions : none
chrom_length
Description : simple getter/setter method for the chromosome length
Parameter[1] : <optional scalar> if specififed it will set the chromsome length
Returntype : scalar
Exceptions : none
display_desc
Description : overrides the superclass method.
returns a debugging description of this instance.
calling display_info() will print this display_desc to STDOUT
Returntype : string
Exceptions : none
xml_start
Description : overrides the superclass method.
returns the start of the XML description of this instance
Returntype : string
Exceptions : none
xml_end
Description : overrides the superclass method.
returns the end tag of the XML description of this instance
Returntype : string
Exceptions : none
xml
Description : overrides the superclass method.
returns the complete XML description of this instance
Returntype : string
Exceptions : none
get_subsequence
Description : uses ChromChunk objects and the sequence in the database to
return the actual sequence in this region. Since the
Chrom is assigned to a specific Assembly one only needs to specify
the start/end and an optional strand to fetch the sequence.
Parameter[1] : chrom_start
the chromosome start of the region to fetch
Parameter[2] : chrom_end
the chromosome end of the region to fetch
Parameter[3] : strand <optional> as "-" or "+"
the strand of the sequence. if "-" then it will return the sequence
on the reverse strand by reverse complementing the sequence
Returntype : Bio::Seq instance or undef if a data error happens
Errors : if the region is not valid or if data is not present it will return undef
Exceptions : none
store
Description : store this instance into an EEDB database
on return the instance will have the primary_id() set.
Parameter[1] : a MQdb::Database to store into
Returntype : $self or undef if a problem occurred
Exceptions : none
update
Description : updates the data of this instance. require the Chrom to have been
fetched from database. It must have database() and primary_id()
Returntype : $self
Exceptions : none